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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatcgataatagacaataactcttaacaacttgtttgtgtgttttgtttgtttctctgtataaccttattttcacttacttttgtgaataaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTTTGAAGATCATCTTATTCTTGGGGAAGAAGGAGGAGTTATAGGAGATGCA

Basic information

species Glycine max
transcript GLYMA06G25880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G25880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G31190.1 (Arabidopsis thaliana), 3'ss of exon 2
-------ataatcgataatagacaataact--cttaacaacttgtttgtgtgttttgtttgtttctctgtataaccttattttcactt--acttttgtgaataaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTTTGAAGATCATCTTATTCTTGGGGAAGAAGGAGGAGTTATAGGAGATGCA
        |  |  |   |  | |||   |  ||| |    ||   | ||| |  ||||   ||   ||  | |   ||||     ||      || |||  || ||  || || ||||||   || || ||||| || || ||||| ||||| |||||||||   ||||||||||||||||| |||||||||||  | || || ||| | 
gtaaggacttcttcaccttttaaaattgttagcttgaggttttaactatgt-tcatgttgacttgattggttgaagctattaaagttttagtacttttgatgaatttgcagTACTGATAAAGCAAGCGAGGCTGCTATTTTGGAAGTAGTGAAGAAGAATTTTAGTGATCATCTTATTCTTGGTGAAGAAGGAGGTATCATCGGCGATTCG

upper sequence: GLYMA06G25880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01800.t01 (Vitis vinifera), 3'ss of exon 3
ataatcgataatagacaataactcttaacaacttgtttgtgtgttttgtttgtttctctgtat----aaccttattttcac-ttacttttgtgaataaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTTTGAAGATCATCTTATTCTTGGGGAAGAAGGAGGAGTTATAGGAGATGCA
       ||| || |   |     |  |    ||   |     |  |||||||  |  || |      |    |||||||| |||  | | || ||  | |  || ||||||||||||||||| ||||| ||  ||||||| || | ||| || |||| |||||| || ||||||||||| || |||||  | || |||||| | 
-----gaatagtatattgttgtggtagattcattcgataaaaataatgtttgtagcaatgaaactcagatgggattttcacattatctatttggatttactgcagCACAGATAAAATGAGTGAGGCTGCTATCCTAGAAGTTGTAAGAAAAAACTTTGGAGATCACCTCATTCTTGGGGAGGAGGGAGGGCTCATCGGAGATACT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|17154103|gb|BM144036.1|BM144036
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|192322372|gb|FK014613.1|FK014613
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|120532442|gb|EH260575.1|EH260575
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|298193777|gb|HO040425.1|HO040425
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|192301816|gb|FG997688.1|FG997688
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|213618101|gb|DB965258.1|DB965258
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
EST: gi|19452428|gb|BM953838.1|BM953838
EST:     AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGA                         GACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT
genomic: AATAAGCCTCGGAATATTACATATAAAGGATTAACTGACTTAGTGACTGAgtaaggtctc ... taaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgtttctctgtataaccttattttcacttacttttgtgaataaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTTTGAAGATCATCTTATTCTTGGGGAAGAAGGAGGAGTTATAGGAGATGCA
                             cacttac  putative branch site (score: 2)
                                ttacttttgtgaataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatcgataatagacaataactcttaacaacttgtttgtgtgttttgtttgtttctctgtataaccttattttcacttacttttgtgaataaattatagGACAGATAAAATGAGTGAAGCTGCCATATTAGAAGTGGTGAAAAAGAATTTTGAAGATCATCTTATTCTTGGGGAAGAAGGAGGAGTTATAGGAGATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG